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Nakanishi H, Pereira V, Børsting C, Tvedebrink T, Takada A, Saito K. Development of an Okinawa panel for biogeographic inference of Okinawans. Ann Hum Biol 2023; 50:436-441. [PMID: 37812250 DOI: 10.1080/03014460.2023.2257594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND The Precision ID Ancestry Panel with 165 SNP markers was unable to differentiate between mainland Japanese and Okinawa Japanese or to distinguish either of them from other East Asian populations. AIM An Okinawa panel was developed with the aim of further separating Okinawa Japanese individuals from mainland Japanese and other Asian groups. Seventy-five SNPs were selected using the most informative markers from the literature. Further, 22 SNPs were selected to separate Okinawa Japanese at minimum SNPs. SUBJECTS AND METHODS Samples were collected from 48 unrelated individuals from mainland Japan and 46 unrelated residents of the Okinawa prefecture. Data were evaluated by STRUCTURE, principal component, and GenoGeographer analyses. RESULTS The 22 SNP set had similar levels of differentiation in STRUCTURE and PCA analyses as the 75 SNP set. GenoGeographer analysis showed that, out of the 46 Okinawa Japanese individuals, the 75 SNP and 22 SNP sets correctly assigned the Okinawan population as the most likely population of origin for 32 and 31 individuals, respectively. CONCLUSION Neither SNP set could completely differentiate between Okinawa Japanese and other Asian groups, however, these sets should be useful for crime investigation, when the sample, cost and time are limited.
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Affiliation(s)
- Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University School of Medicine, Tokyo, Japan
- Department of Forensic Medicine, Saitama Medical University, Saitama, Japan
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Tvedebrink
- Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark
| | - Aya Takada
- Department of Forensic Medicine, Saitama Medical University, Saitama, Japan
| | - Kazuyuki Saito
- Department of Forensic Medicine, Juntendo University School of Medicine, Tokyo, Japan
- Department of Forensic Medicine, Saitama Medical University, Saitama, Japan
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Gakuhari T, Nakagome S, Rasmussen S, Allentoft ME, Sato T, Korneliussen T, Chuinneagáin BN, Matsumae H, Koganebuchi K, Schmidt R, Mizushima S, Kondo O, Shigehara N, Yoneda M, Kimura R, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Tsurumoto T, Wakebe T, Shitara H, Hanihara T, Willerslev E, Sikora M, Oota H. Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations. Commun Biol 2020; 3:437. [PMID: 32843717 PMCID: PMC7447786 DOI: 10.1038/s42003-020-01162-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 07/16/2020] [Indexed: 12/28/2022] Open
Abstract
Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia. Takashi Gakuhari, Shigeki Nakagome et al. report the genomic analysis on a 2.5 kya individual from the ancient Jomon culture in present-day Japan. Phylogenetic analysis with comparison to other Eurasian sequences suggests early migration patterns in Asia and provides insight into the genetic affinities between peoples of the region.
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Affiliation(s)
- Takashi Gakuhari
- Center for Cultural Resource Studies, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan.,Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan.,Kitasato University School of Medicine, Sagamihara, Japan
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, the University of Dublin, Dublin, Ireland
| | - Simon Rasmussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Trace and Environmental DNA (TrEnD) laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Ryan Schmidt
- Kitasato University School of Medicine, Sagamihara, Japan
| | - Souichiro Mizushima
- Department of Anatomy, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Osamu Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nobuo Shigehara
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Hajime Ishida
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | | | | | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Toshiyuki Tsurumoto
- Department of Macroscopic Anatomy, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan
| | - Tetsuaki Wakebe
- Department of Macroscopic Anatomy, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan
| | - Hiromi Shitara
- Department of Archaeology, The University of Tokyo, Tokyo, Japan
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,GeoGenetics Groups, Department of Zoology, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Hiroki Oota
- Kitasato University School of Medicine, Sagamihara, Japan. .,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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Yuasa I, Akane A, Yamamoto T, Matsusue A, Endoh M, Nakagawa M, Umetsu K, Ishikawa T, Iino M. Japaneseplex: A forensic SNP assay for identification of Japanese people using Japanese-specific alleles. Leg Med (Tokyo) 2018; 33:17-22. [PMID: 29705644 DOI: 10.1016/j.legalmed.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 02/15/2018] [Accepted: 04/23/2018] [Indexed: 11/17/2022]
Abstract
It is sometimes necessary to determine whether a forensic biological sample came from a Japanese person. In this study, we developed a 60-locus SNP assay designed for the differentiation of Japanese people from other East Asians using entirely and nearly Japanese-specific alleles. This multiplex assay consisted of 6 independent PCR reactions followed by single nucleotide extension. The average number and standard deviation of Japanese-specific alleles possessed by an individual were 0.81 ± 0.93 in 108 Koreans from Seoul, 8.87 ± 2.89 in 103 Japanese from Tottori, 17.20 ± 3.80 in 88 Japanese from Okinawa, and 0 in 220 Han Chinese from Wuxi and Changsha. The Koreans had 0-4 Japanese-specific alleles per individual, whereas the Japanese had 4-26 Japanese-specific alleles. Almost all Japanese were distinguished from the Koreans and other people by the factorial correspondence and principal component analyses. The Snipper program was also useful to estimate the degree of Japaneseness. The method described here was successfully applied to the differentiation of Japanese from non-Japanese people in forensic cases. This Japanese-specific SNP assay was named Japaneseplex.
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Affiliation(s)
- Isao Yuasa
- Division of Legal Medicine, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan.
| | - Atsushi Akane
- Department of Legal Medicine, Kansai Medical University, Hirakata, Japan
| | - Toshimichi Yamamoto
- Department of Legal Medicine and Bioethics, Nagoya University School of Medicine, Nagoya, Japan
| | - Aya Matsusue
- Department of Forensic Medicine, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Minoru Endoh
- Division of Legal Medicine, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
| | - Mayumi Nakagawa
- Department of Pathobiological Science and Technology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Kazuo Umetsu
- Department of Forensic Medicine, Yamagata University School of Medicine, Yamagata, Japan
| | - Takaki Ishikawa
- Department of Legal Medicine, Osaka City University Medical School, Osaka, Japan
| | - Morio Iino
- Division of Legal Medicine, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
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